Absolute enrichment: gene set enrichment analysis for homeostatic systems

The Gene Set Enrichment Analysis (GSEA) identifies sets of genes that are differentially regulated in one direction. Many homeostatic systems will include one limb that is upregulated in response to a downregulation of another limb and vice versa. Such patterns are poorly captured by the standard formulation of GSEA. We describe a technique to identify groups of genes (which sometimes can be pathways) that include both up- and down-regulated components. This approach lends insights into the feedback mechanisms that may operate, especially when integrated with protein interaction databases.     

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

ABSTRACT: BACKGROUND: Gene-set enrichment analyses (GEA or GSEA) are commonly used for biological characterization of an experimental gene-set. This is done by finding known functional categories, such as pathways or Gene Ontology terms, that are over-represented in the experimental set; the assessment is based on an overlap statistic. Rich biological information in terms of gene interaction network is now widely available, but this topological information is not used by GEA, so there is a need for methods that exploit this type of information in high-throughput data analysis. RESULTS: We developed a method of network enrichment analysis (NEA) that extends the overlap statistic in GEA to network links between genes in the experimental set and those in the functional categories. For the crucial step in statistical inference, we developed a fast network randomization algorithm in order to obtain the distribution of any network statistic under the null hypothesis of no association between an experimental gene-set and a functional category. We illustrate the NEA method using gene and protein expression data from a lung cancer study. CONCLUSIONS: The results indicate that the NEA method is more powerful than the traditional GEA, primarily because the relationships between gene sets were more strongly captured by network connectivity rather than by simple overlaps.     

Neural consequences of environmental enrichment

Neuronal plasticity is a central theme of modern neurobiology, from cellular and molecular mechanisms of synapse formation in Drosophila to behavioural recovery from strokes in elderly humans. Although the methods used to measure plastic responses differ, the stimuli required to elicit plasticity are thought to be activity-dependent. In this article, we focus on the neuronal changes that occur in response to complex stimulation by an enriched environment. We emphasize the behavioural and neurobiological consequences of specific elements of enrichment, especially exercise and learning.     

Effects of environmental enrichment on reproduction

Although there have been few demonstrations of a direct empirical relationship between environmental enrichment and reproductive success in captive animals, indirect and anecdotal evidence indicates the importance of physical and temporal complexity for reproduction. We discuss three major mechanisms through which environmental enrichment that specifically increases the complexity of an animal's surroundings may influence reproductive physiology and behavior: developmental processes, modulation of stress and arousal, and modification of social interactions. In complex environments developing animals learn that performing active behavior produces appropriate functional outcomes. Learning to control their environment influences their ability to adapt to novel situations, which may profoundly influence their reproductive behavior as adults in breeding situations. Chronic stress may compromise reproductive physiology and behavior; enrichment reduces stress by providing increased opportunity for behavioral coping responses. However, some degree of acute stress may be beneficial for reproduction by maintaining an animal's level of responsiveness to socio-sexual stimuli necessary for sexual arousal and reproductive activation. Finally, environmental enrichment may influence reproductive success by stabilizing social groups, reducing aggression and increasing affiliative and play behaviors. It is concluded that multi-variate multi-institutional behavioral research in zoos will play an increasingly important role in the successful captive propagation of many species by closely examining relationships between environmental variables and reproductive potential of individual animals. © 1994 Wiley-Liss, Inc.     

Types of enrichment axes in Poaceae

The objective of this review work is to characterize the enrichment axes in Poaceae, especially integrating into that analysis of those species with basal or subterranean cleistogamous spikelets. We recognize five types of enrichment axes: paraclades of the unit of inflorescence (UIF), paraclades of the trophotagma (TT) with exposed UIF; paraclades of the trophotagma with not exposed UIF; subterranean paraclades on short rhizomes and subterranean paraclades upon plagiotropic axes of long internodes. According to the enrichment axes, we differentiate six types of synflorescences. The different types of enrichment axes and synflorescences types are characterized; their differences determine in some cases the existence of fruit heteromorphism.     

Evaluation of a chimpanzee enrichment enclosure

A large, three-part playground for captive chimpanzees was constructed and evaluated in terms of area use and behavior changes. Comparative behavioral samples were obtained on 38 subjects in the existing indoor-outdoor run and in the enclosure. The chimpanzees used the inside run, connective chute, concrete slab, and grass areas most. Activity and environmental manipulation increased in the enclosure while abnormal and self-directed behaviors decreased.     

Environmental enrichment for zoo bears

The high incidence of stereotypic behaviors in zoo bears (van Keulen-Kromhout: International Zoo Yearbook 18:177–186, 1978) suggests that the environment of these animals lacks essential stimuli for guiding normal behavior. Three experiments investigated ways in which bear husbandry procedures can be altered to promote normal behavior. In experiments 1 and 2, honey-filled logs were given to a sloth (Melursus ursinus), American black (Ursus americanus), and brown bear (Ursus arctos) to determine 1) the role of food in stimulating investigatory behavior, 2) the rate of habituation to manipulable objects introduced into the exhibit, and 3) effects on locomotory behaviors. Results show specific and general habituation to the introduced objects that can be counteracted by refilling the logs with honey and by providing multiple logs in the exhibit. Investigatory activity directed toward honey-logs replaces pacing and walking in the sloth bear and is most effective in doing so when the log is novel. Experiment 3 examined the behavioral effects of feeding an American black bear in three different ways: 1) once daily in the den, 2) once daily with supplemental food from a mechanical feeder, and 3) once daily with food hidden in the exhibit in manipulatable objects. The latter method reduced stereotypic pacing from a median of 150 min/day to 20 min/day; the mechanical feeder method had no such effect. The results of a survey of 67 zoos concerning the diet and manner of feeding these three species of bears, as well as Asian black bears (Ursus thibetanus) are presented. Results are discussed with respect to the ways in which husbandry procedures can be improved to stimulate functional foraging and feeding behavior in confined bears.     

厌氧氨氧化菌富集培养物对羟胺的转化研究

【目的】羟胺是厌氧氨氧化的重要中间产物,本研究旨在探明厌氧氨氧化菌对羟胺的转化特性。【方法】采用厌氧氨氧化菌富集培养物,以羟胺和亚硝酸盐为基质进行分批培养试验,检测反应液中基质和产物的消涨情况。【结果】不接种厌氧氨氧化富集培养物时,羟胺和亚硝酸盐具有化学稳定性,彼此不发生化学反应;接种厌氧氨氧化富集培养物后,羟胺和亚硝酸盐发生化学反应;反应过程中有中间产物氨的产生和转化,最大氨氮积累浓度为0.338mmol/L;液相中总氮浓度从起始的4.694mmol/L降至结束时的0.812mmol/L,转化率为82.7%。羟胺和亚硝氮浓度均为2.5mmol/L时,羟胺最大比污泥转化速率为0.535mmol/(gVSS.h),是厌氧氨氧化反应体系中氨氮最大比污泥转化速率的1.81倍。将羟胺浓度提高至5.0mmol/L时,羟胺和亚硝氮转化速率分别提高26.7%和120.7%,最大氨氮积累浓度为0.795mmol/L;将亚硝氮浓度提高至5.0mmol/L时,羟胺和亚硝氮转化速率分别提高6.9%和9.0%,最大氨氮积累浓度为1.810mmol/L。【结论】厌氧氨氧化富集培养物能够转化羟胺,其对羟胺的转化速率高于对氨的转化速率。羟胺相对过量可显著加快羟胺和亚硝酸盐的转化速率,亚硝酸盐相对过量对羟胺和亚硝氮转化速率影响不大,提高羟胺或亚硝氮浓度均会增大中间产物氨氮的积累。实验现象可用van de Graaf模型解释,对于进一步开发厌氧氨氧化工艺具有重要的理论意义。     

Alteration of phytoplankton phosphorus status during enrichment experiments: implications for interpreting nutrient enrichment bioassay results

We compared the results of phosphorus-enrichment bioassay experiments with alkaline phosphatase activity (APA) assays as indicators of phosphorus (P) limitation of in situ phytoplankton growth. In 4-d experiments, phytoplankton APA decreased or remained unchanged in P-enriched samples, but increased in unenriched samples, indicating a rapid alteration of the P status of the unenriched algae during the experimental incubations. In direct comparisons of enrichment bioassays and APA assays of reservoir phytoplankton samples, the results of the two methods corresponded in general, although contradictory results were not uncommon. Our data support the conclusion that enrichment experiments can indicate the potential for nutrient limitation of algal growth in the absence of other limiting factors, but do not necessarily demonstrate the occurrence of in situ nutrient limitation of phytoplankton production.     

Enrichment Disequilibrium: A novel approach for measuring the degree of enrichment after gene enrichment test

Motivation: Commonly used gene enrichment analysis methods, such as Hypergeometric distribution, play an important role in the functional analysis of interesting gene lists. But the statistical significance obtained by these methods only represents the probability of error that is involved in accepting enrichment, and is not suitable to evaluate the degree of enrichment. Although there have been some methods to measure the enrichment degrees, such as relative enrichment factor, new methods are still needed to meet the requirements for comparing the degree of enrichment. Results: We developed a novel method, Enrichment Disequilibrium (ED), to measure the degree of enrichment. Enrichment equilibrium means that the interesting gene set and the known functional gene set (such as a KEGG pathway) are independent (i.e. random association). ED is defined as the degree of non-independence. Compared with the relative enrichment factor, ED has a clearer biological meaning, is a standardized indicator, and has a symmetrical interval (range from -1 to +1). It is more suitable to measure the enrichment degree. For an interesting gene set, researchers can obtain some significant functional gene sets by traditional enrichment test. Then using ED, they can compare the degree of enrichment among these significant gene sets, and prioritize them.     

Environmental enrichment for captive animals

A review of "Second Nature: Environmental Enrichment for Captive Animals," edited by David J. Shepherson, Jill D. Mellen, and Michael Hutchins. Washington, DC: Smithsonian Press, 1998, 350pp., $32.50, hardbound; $17.95 paperback.